"""Bagging meta-estimator.""" # Author: Gilles Louppe # License: BSD 3 clause from __future__ import division import itertools import numbers import numpy as np from warnings import warn from abc import ABCMeta, abstractmethod from ..base import ClassifierMixin, RegressorMixin from ..externals.joblib import Parallel, delayed from ..externals.six import with_metaclass from ..externals.six.moves import zip from ..metrics import r2_score, accuracy_score from ..tree import DecisionTreeClassifier, DecisionTreeRegressor from ..utils import check_random_state, check_X_y, check_array, column_or_1d from ..utils.random import sample_without_replacement from ..utils.validation import has_fit_parameter, check_is_fitted from ..utils import indices_to_mask, check_consistent_length from ..utils.metaestimators import if_delegate_has_method from ..utils.multiclass import check_classification_targets from .base import BaseEnsemble, _partition_estimators __all__ = ["BaggingClassifier", "BaggingRegressor"] MAX_INT = np.iinfo(np.int32).max def _generate_indices(random_state, bootstrap, n_population, n_samples): """Draw randomly sampled indices.""" # Draw sample indices if bootstrap: indices = random_state.randint(0, n_population, n_samples) else: indices = sample_without_replacement(n_population, n_samples, random_state=random_state) return indices def _generate_bagging_indices(random_state, bootstrap_features, bootstrap_samples, n_features, n_samples, max_features, max_samples): """Randomly draw feature and sample indices.""" # Get valid random state random_state = check_random_state(random_state) # Draw indices feature_indices = _generate_indices(random_state, bootstrap_features, n_features, max_features) sample_indices = _generate_indices(random_state, bootstrap_samples, n_samples, max_samples) return feature_indices, sample_indices def _parallel_build_estimators(n_estimators, ensemble, X, y, sample_weight, seeds, total_n_estimators, verbose): """Private function used to build a batch of estimators within a job.""" # Retrieve settings n_samples, n_features = X.shape max_features = ensemble._max_features max_samples = ensemble._max_samples bootstrap = ensemble.bootstrap bootstrap_features = ensemble.bootstrap_features support_sample_weight = has_fit_parameter(ensemble.base_estimator_, "sample_weight") if not support_sample_weight and sample_weight is not None: raise ValueError("The base estimator doesn't support sample weight") # Build estimators estimators = [] estimators_features = [] for i in range(n_estimators): if verbose > 1: print("Building estimator %d of %d for this parallel run " "(total %d)..." % (i + 1, n_estimators, total_n_estimators)) random_state = np.random.RandomState(seeds[i]) estimator = ensemble._make_estimator(append=False, random_state=random_state) # Draw random feature, sample indices features, indices = _generate_bagging_indices(random_state, bootstrap_features, bootstrap, n_features, n_samples, max_features, max_samples) # Draw samples, using sample weights, and then fit if support_sample_weight: if sample_weight is None: curr_sample_weight = np.ones((n_samples,)) else: curr_sample_weight = sample_weight.copy() if bootstrap: sample_counts = np.bincount(indices, minlength=n_samples) curr_sample_weight *= sample_counts else: not_indices_mask = ~indices_to_mask(indices, n_samples) curr_sample_weight[not_indices_mask] = 0 estimator.fit(X[:, features], y, sample_weight=curr_sample_weight) # Draw samples, using a mask, and then fit else: estimator.fit((X[indices])[:, features], y[indices]) estimators.append(estimator) estimators_features.append(features) return estimators, estimators_features def _parallel_predict_proba(estimators, estimators_features, X, n_classes): """Private function used to compute (proba-)predictions within a job.""" n_samples = X.shape[0] proba = np.zeros((n_samples, n_classes)) for estimator, features in zip(estimators, estimators_features): if hasattr(estimator, "predict_proba"): proba_estimator = estimator.predict_proba(X[:, features]) if n_classes == len(estimator.classes_): proba += proba_estimator else: proba[:, estimator.classes_] += \ proba_estimator[:, range(len(estimator.classes_))] else: # Resort to voting predictions = estimator.predict(X[:, features]) for i in range(n_samples): proba[i, predictions[i]] += 1 return proba def _parallel_predict_log_proba(estimators, estimators_features, X, n_classes): """Private function used to compute log probabilities within a job.""" n_samples = X.shape[0] log_proba = np.empty((n_samples, n_classes)) log_proba.fill(-np.inf) all_classes = np.arange(n_classes, dtype=np.int) for estimator, features in zip(estimators, estimators_features): log_proba_estimator = estimator.predict_log_proba(X[:, features]) if n_classes == len(estimator.classes_): log_proba = np.logaddexp(log_proba, log_proba_estimator) else: log_proba[:, estimator.classes_] = np.logaddexp( log_proba[:, estimator.classes_], log_proba_estimator[:, range(len(estimator.classes_))]) missing = np.setdiff1d(all_classes, estimator.classes_) log_proba[:, missing] = np.logaddexp(log_proba[:, missing], -np.inf) return log_proba def _parallel_decision_function(estimators, estimators_features, X): """Private function used to compute decisions within a job.""" return sum(estimator.decision_function(X[:, features]) for estimator, features in zip(estimators, estimators_features)) def _parallel_predict_regression(estimators, estimators_features, X): """Private function used to compute predictions within a job.""" return sum(estimator.predict(X[:, features]) for estimator, features in zip(estimators, estimators_features)) class BaseBagging(with_metaclass(ABCMeta, BaseEnsemble)): """Base class for Bagging meta-estimator. Warning: This class should not be used directly. Use derived classes instead. """ @abstractmethod def __init__(self, base_estimator=None, n_estimators=10, max_samples=1.0, max_features=1.0, bootstrap=True, bootstrap_features=False, oob_score=False, warm_start=False, n_jobs=1, random_state=None, verbose=0): super(BaseBagging, self).__init__( base_estimator=base_estimator, n_estimators=n_estimators) self.max_samples = max_samples self.max_features = max_features self.bootstrap = bootstrap self.bootstrap_features = bootstrap_features self.oob_score = oob_score self.warm_start = warm_start self.n_jobs = n_jobs self.random_state = random_state self.verbose = verbose def fit(self, X, y, sample_weight=None): """Build a Bagging ensemble of estimators from the training set (X, y). Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. y : array-like, shape = [n_samples] The target values (class labels in classification, real numbers in regression). sample_weight : array-like, shape = [n_samples] or None Sample weights. If None, then samples are equally weighted. Note that this is supported only if the base estimator supports sample weighting. Returns ------- self : object Returns self. """ return self._fit(X, y, self.max_samples, sample_weight=sample_weight) def _fit(self, X, y, max_samples=None, max_depth=None, sample_weight=None): """Build a Bagging ensemble of estimators from the training set (X, y). Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. y : array-like, shape = [n_samples] The target values (class labels in classification, real numbers in regression). max_samples : int or float, optional (default=None) Argument to use instead of self.max_samples. max_depth : int, optional (default=None) Override value used when constructing base estimator. Only supported if the base estimator has a max_depth parameter. sample_weight : array-like, shape = [n_samples] or None Sample weights. If None, then samples are equally weighted. Note that this is supported only if the base estimator supports sample weighting. Returns ------- self : object Returns self. """ random_state = check_random_state(self.random_state) # Convert data X, y = check_X_y(X, y, ['csr', 'csc']) if sample_weight is not None: sample_weight = check_array(sample_weight, ensure_2d=False) check_consistent_length(y, sample_weight) # Remap output n_samples, self.n_features_ = X.shape self._n_samples = n_samples y = self._validate_y(y) # Check parameters self._validate_estimator() if max_depth is not None: self.base_estimator_.max_depth = max_depth # Validate max_samples if max_samples is None: max_samples = self.max_samples elif not isinstance(max_samples, (numbers.Integral, np.integer)): max_samples = int(max_samples * X.shape[0]) if not (0 < max_samples <= X.shape[0]): raise ValueError("max_samples must be in (0, n_samples]") # Store validated integer row sampling value self._max_samples = max_samples # Validate max_features if isinstance(self.max_features, (numbers.Integral, np.integer)): max_features = self.max_features else: # float max_features = int(self.max_features * self.n_features_) if not (0 < max_features <= self.n_features_): raise ValueError("max_features must be in (0, n_features]") # Store validated integer feature sampling value self._max_features = max_features # Other checks if not self.bootstrap and self.oob_score: raise ValueError("Out of bag estimation only available" " if bootstrap=True") if self.warm_start and self.oob_score: raise ValueError("Out of bag estimate only available" " if warm_start=False") if hasattr(self, "oob_score_") and self.warm_start: del self.oob_score_ if not self.warm_start or not hasattr(self, 'estimators_'): # Free allocated memory, if any self.estimators_ = [] self.estimators_features_ = [] n_more_estimators = self.n_estimators - len(self.estimators_) if n_more_estimators < 0: raise ValueError('n_estimators=%d must be larger or equal to ' 'len(estimators_)=%d when warm_start==True' % (self.n_estimators, len(self.estimators_))) elif n_more_estimators == 0: warn("Warm-start fitting without increasing n_estimators does not " "fit new trees.") return self # Parallel loop n_jobs, n_estimators, starts = _partition_estimators(n_more_estimators, self.n_jobs) total_n_estimators = sum(n_estimators) # Advance random state to state after training # the first n_estimators if self.warm_start and len(self.estimators_) > 0: random_state.randint(MAX_INT, size=len(self.estimators_)) seeds = random_state.randint(MAX_INT, size=n_more_estimators) self._seeds = seeds all_results = Parallel(n_jobs=n_jobs, verbose=self.verbose)( delayed(_parallel_build_estimators)( n_estimators[i], self, X, y, sample_weight, seeds[starts[i]:starts[i + 1]], total_n_estimators, verbose=self.verbose) for i in range(n_jobs)) # Reduce self.estimators_ += list(itertools.chain.from_iterable( t[0] for t in all_results)) self.estimators_features_ += list(itertools.chain.from_iterable( t[1] for t in all_results)) if self.oob_score: self._set_oob_score(X, y) return self @abstractmethod def _set_oob_score(self, X, y): """Calculate out of bag predictions and score.""" def _validate_y(self, y): # Default implementation return column_or_1d(y, warn=True) def _get_estimators_indices(self): # Get drawn indices along both sample and feature axes for seed in self._seeds: # Operations accessing random_state must be performed identically # to those in `_parallel_build_estimators()` random_state = np.random.RandomState(seed) feature_indices, sample_indices = _generate_bagging_indices( random_state, self.bootstrap_features, self.bootstrap, self.n_features_, self._n_samples, self._max_features, self._max_samples) yield feature_indices, sample_indices @property def estimators_samples_(self): """The subset of drawn samples for each base estimator. Returns a dynamically generated list of boolean masks identifying the samples used for fitting each member of the ensemble, i.e., the in-bag samples. Note: the list is re-created at each call to the property in order to reduce the object memory footprint by not storing the sampling data. Thus fetching the property may be slower than expected. """ sample_masks = [] for _, sample_indices in self._get_estimators_indices(): mask = indices_to_mask(sample_indices, self._n_samples) sample_masks.append(mask) return sample_masks class BaggingClassifier(BaseBagging, ClassifierMixin): """A Bagging classifier. A Bagging classifier is an ensemble meta-estimator that fits base classifiers each on random subsets of the original dataset and then aggregate their individual predictions (either by voting or by averaging) to form a final prediction. Such a meta-estimator can typically be used as a way to reduce the variance of a black-box estimator (e.g., a decision tree), by introducing randomization into its construction procedure and then making an ensemble out of it. This algorithm encompasses several works from the literature. When random subsets of the dataset are drawn as random subsets of the samples, then this algorithm is known as Pasting [1]_. If samples are drawn with replacement, then the method is known as Bagging [2]_. When random subsets of the dataset are drawn as random subsets of the features, then the method is known as Random Subspaces [3]_. Finally, when base estimators are built on subsets of both samples and features, then the method is known as Random Patches [4]_. Read more in the :ref:`User Guide `. Parameters ---------- base_estimator : object or None, optional (default=None) The base estimator to fit on random subsets of the dataset. If None, then the base estimator is a decision tree. n_estimators : int, optional (default=10) The number of base estimators in the ensemble. max_samples : int or float, optional (default=1.0) The number of samples to draw from X to train each base estimator. - If int, then draw `max_samples` samples. - If float, then draw `max_samples * X.shape[0]` samples. max_features : int or float, optional (default=1.0) The number of features to draw from X to train each base estimator. - If int, then draw `max_features` features. - If float, then draw `max_features * X.shape[1]` features. bootstrap : boolean, optional (default=True) Whether samples are drawn with replacement. bootstrap_features : boolean, optional (default=False) Whether features are drawn with replacement. oob_score : bool Whether to use out-of-bag samples to estimate the generalization error. warm_start : bool, optional (default=False) When set to True, reuse the solution of the previous call to fit and add more estimators to the ensemble, otherwise, just fit a whole new ensemble. .. versionadded:: 0.17 *warm_start* constructor parameter. n_jobs : int, optional (default=1) The number of jobs to run in parallel for both `fit` and `predict`. If -1, then the number of jobs is set to the number of cores. random_state : int, RandomState instance or None, optional (default=None) If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by `np.random`. verbose : int, optional (default=0) Controls the verbosity of the building process. Attributes ---------- base_estimator_ : estimator The base estimator from which the ensemble is grown. estimators_ : list of estimators The collection of fitted base estimators. estimators_samples_ : list of arrays The subset of drawn samples (i.e., the in-bag samples) for each base estimator. Each subset is defined by a boolean mask. estimators_features_ : list of arrays The subset of drawn features for each base estimator. classes_ : array of shape = [n_classes] The classes labels. n_classes_ : int or list The number of classes. oob_score_ : float Score of the training dataset obtained using an out-of-bag estimate. oob_decision_function_ : array of shape = [n_samples, n_classes] Decision function computed with out-of-bag estimate on the training set. If n_estimators is small it might be possible that a data point was never left out during the bootstrap. In this case, `oob_decision_function_` might contain NaN. References ---------- .. [1] L. Breiman, "Pasting small votes for classification in large databases and on-line", Machine Learning, 36(1), 85-103, 1999. .. [2] L. Breiman, "Bagging predictors", Machine Learning, 24(2), 123-140, 1996. .. [3] T. Ho, "The random subspace method for constructing decision forests", Pattern Analysis and Machine Intelligence, 20(8), 832-844, 1998. .. [4] G. Louppe and P. Geurts, "Ensembles on Random Patches", Machine Learning and Knowledge Discovery in Databases, 346-361, 2012. """ def __init__(self, base_estimator=None, n_estimators=10, max_samples=1.0, max_features=1.0, bootstrap=True, bootstrap_features=False, oob_score=False, warm_start=False, n_jobs=1, random_state=None, verbose=0): super(BaggingClassifier, self).__init__( base_estimator, n_estimators=n_estimators, max_samples=max_samples, max_features=max_features, bootstrap=bootstrap, bootstrap_features=bootstrap_features, oob_score=oob_score, warm_start=warm_start, n_jobs=n_jobs, random_state=random_state, verbose=verbose) def _validate_estimator(self): """Check the estimator and set the base_estimator_ attribute.""" super(BaggingClassifier, self)._validate_estimator( default=DecisionTreeClassifier()) def _set_oob_score(self, X, y): n_samples = y.shape[0] n_classes_ = self.n_classes_ classes_ = self.classes_ predictions = np.zeros((n_samples, n_classes_)) for estimator, samples, features in zip(self.estimators_, self.estimators_samples_, self.estimators_features_): # Create mask for OOB samples mask = ~samples if hasattr(estimator, "predict_proba"): predictions[mask, :] += estimator.predict_proba( (X[mask, :])[:, features]) else: p = estimator.predict((X[mask, :])[:, features]) j = 0 for i in range(n_samples): if mask[i]: predictions[i, p[j]] += 1 j += 1 if (predictions.sum(axis=1) == 0).any(): warn("Some inputs do not have OOB scores. " "This probably means too few estimators were used " "to compute any reliable oob estimates.") oob_decision_function = (predictions / predictions.sum(axis=1)[:, np.newaxis]) oob_score = accuracy_score(y, np.argmax(predictions, axis=1)) self.oob_decision_function_ = oob_decision_function self.oob_score_ = oob_score def _validate_y(self, y): y = column_or_1d(y, warn=True) check_classification_targets(y) self.classes_, y = np.unique(y, return_inverse=True) self.n_classes_ = len(self.classes_) return y def predict(self, X): """Predict class for X. The predicted class of an input sample is computed as the class with the highest mean predicted probability. If base estimators do not implement a ``predict_proba`` method, then it resorts to voting. Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. Returns ------- y : array of shape = [n_samples] The predicted classes. """ predicted_probabilitiy = self.predict_proba(X) return self.classes_.take((np.argmax(predicted_probabilitiy, axis=1)), axis=0) def predict_proba(self, X): """Predict class probabilities for X. The predicted class probabilities of an input sample is computed as the mean predicted class probabilities of the base estimators in the ensemble. If base estimators do not implement a ``predict_proba`` method, then it resorts to voting and the predicted class probabilities of an input sample represents the proportion of estimators predicting each class. Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. Returns ------- p : array of shape = [n_samples, n_classes] The class probabilities of the input samples. The order of the classes corresponds to that in the attribute `classes_`. """ check_is_fitted(self, "classes_") # Check data X = check_array(X, accept_sparse=['csr', 'csc']) if self.n_features_ != X.shape[1]: raise ValueError("Number of features of the model must " "match the input. Model n_features is {0} and " "input n_features is {1}." "".format(self.n_features_, X.shape[1])) # Parallel loop n_jobs, n_estimators, starts = _partition_estimators(self.n_estimators, self.n_jobs) all_proba = Parallel(n_jobs=n_jobs, verbose=self.verbose)( delayed(_parallel_predict_proba)( self.estimators_[starts[i]:starts[i + 1]], self.estimators_features_[starts[i]:starts[i + 1]], X, self.n_classes_) for i in range(n_jobs)) # Reduce proba = sum(all_proba) / self.n_estimators return proba def predict_log_proba(self, X): """Predict class log-probabilities for X. The predicted class log-probabilities of an input sample is computed as the log of the mean predicted class probabilities of the base estimators in the ensemble. Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. Returns ------- p : array of shape = [n_samples, n_classes] The class log-probabilities of the input samples. The order of the classes corresponds to that in the attribute `classes_`. """ check_is_fitted(self, "classes_") if hasattr(self.base_estimator_, "predict_log_proba"): # Check data X = check_array(X, accept_sparse=['csr', 'csc']) if self.n_features_ != X.shape[1]: raise ValueError("Number of features of the model must " "match the input. Model n_features is {0} " "and input n_features is {1} " "".format(self.n_features_, X.shape[1])) # Parallel loop n_jobs, n_estimators, starts = _partition_estimators( self.n_estimators, self.n_jobs) all_log_proba = Parallel(n_jobs=n_jobs, verbose=self.verbose)( delayed(_parallel_predict_log_proba)( self.estimators_[starts[i]:starts[i + 1]], self.estimators_features_[starts[i]:starts[i + 1]], X, self.n_classes_) for i in range(n_jobs)) # Reduce log_proba = all_log_proba[0] for j in range(1, len(all_log_proba)): log_proba = np.logaddexp(log_proba, all_log_proba[j]) log_proba -= np.log(self.n_estimators) return log_proba else: return np.log(self.predict_proba(X)) @if_delegate_has_method(delegate='base_estimator') def decision_function(self, X): """Average of the decision functions of the base classifiers. Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. Returns ------- score : array, shape = [n_samples, k] The decision function of the input samples. The columns correspond to the classes in sorted order, as they appear in the attribute ``classes_``. Regression and binary classification are special cases with ``k == 1``, otherwise ``k==n_classes``. """ check_is_fitted(self, "classes_") # Check data X = check_array(X, accept_sparse=['csr', 'csc']) if self.n_features_ != X.shape[1]: raise ValueError("Number of features of the model must " "match the input. Model n_features is {0} and " "input n_features is {1} " "".format(self.n_features_, X.shape[1])) # Parallel loop n_jobs, n_estimators, starts = _partition_estimators(self.n_estimators, self.n_jobs) all_decisions = Parallel(n_jobs=n_jobs, verbose=self.verbose)( delayed(_parallel_decision_function)( self.estimators_[starts[i]:starts[i + 1]], self.estimators_features_[starts[i]:starts[i + 1]], X) for i in range(n_jobs)) # Reduce decisions = sum(all_decisions) / self.n_estimators return decisions class BaggingRegressor(BaseBagging, RegressorMixin): """A Bagging regressor. A Bagging regressor is an ensemble meta-estimator that fits base regressors each on random subsets of the original dataset and then aggregate their individual predictions (either by voting or by averaging) to form a final prediction. Such a meta-estimator can typically be used as a way to reduce the variance of a black-box estimator (e.g., a decision tree), by introducing randomization into its construction procedure and then making an ensemble out of it. This algorithm encompasses several works from the literature. When random subsets of the dataset are drawn as random subsets of the samples, then this algorithm is known as Pasting [1]_. If samples are drawn with replacement, then the method is known as Bagging [2]_. When random subsets of the dataset are drawn as random subsets of the features, then the method is known as Random Subspaces [3]_. Finally, when base estimators are built on subsets of both samples and features, then the method is known as Random Patches [4]_. Read more in the :ref:`User Guide `. Parameters ---------- base_estimator : object or None, optional (default=None) The base estimator to fit on random subsets of the dataset. If None, then the base estimator is a decision tree. n_estimators : int, optional (default=10) The number of base estimators in the ensemble. max_samples : int or float, optional (default=1.0) The number of samples to draw from X to train each base estimator. - If int, then draw `max_samples` samples. - If float, then draw `max_samples * X.shape[0]` samples. max_features : int or float, optional (default=1.0) The number of features to draw from X to train each base estimator. - If int, then draw `max_features` features. - If float, then draw `max_features * X.shape[1]` features. bootstrap : boolean, optional (default=True) Whether samples are drawn with replacement. bootstrap_features : boolean, optional (default=False) Whether features are drawn with replacement. oob_score : bool Whether to use out-of-bag samples to estimate the generalization error. warm_start : bool, optional (default=False) When set to True, reuse the solution of the previous call to fit and add more estimators to the ensemble, otherwise, just fit a whole new ensemble. n_jobs : int, optional (default=1) The number of jobs to run in parallel for both `fit` and `predict`. If -1, then the number of jobs is set to the number of cores. random_state : int, RandomState instance or None, optional (default=None) If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by `np.random`. verbose : int, optional (default=0) Controls the verbosity of the building process. Attributes ---------- estimators_ : list of estimators The collection of fitted sub-estimators. estimators_samples_ : list of arrays The subset of drawn samples (i.e., the in-bag samples) for each base estimator. Each subset is defined by a boolean mask. estimators_features_ : list of arrays The subset of drawn features for each base estimator. oob_score_ : float Score of the training dataset obtained using an out-of-bag estimate. oob_prediction_ : array of shape = [n_samples] Prediction computed with out-of-bag estimate on the training set. If n_estimators is small it might be possible that a data point was never left out during the bootstrap. In this case, `oob_prediction_` might contain NaN. References ---------- .. [1] L. Breiman, "Pasting small votes for classification in large databases and on-line", Machine Learning, 36(1), 85-103, 1999. .. [2] L. Breiman, "Bagging predictors", Machine Learning, 24(2), 123-140, 1996. .. [3] T. Ho, "The random subspace method for constructing decision forests", Pattern Analysis and Machine Intelligence, 20(8), 832-844, 1998. .. [4] G. Louppe and P. Geurts, "Ensembles on Random Patches", Machine Learning and Knowledge Discovery in Databases, 346-361, 2012. """ def __init__(self, base_estimator=None, n_estimators=10, max_samples=1.0, max_features=1.0, bootstrap=True, bootstrap_features=False, oob_score=False, warm_start=False, n_jobs=1, random_state=None, verbose=0): super(BaggingRegressor, self).__init__( base_estimator, n_estimators=n_estimators, max_samples=max_samples, max_features=max_features, bootstrap=bootstrap, bootstrap_features=bootstrap_features, oob_score=oob_score, warm_start=warm_start, n_jobs=n_jobs, random_state=random_state, verbose=verbose) def predict(self, X): """Predict regression target for X. The predicted regression target of an input sample is computed as the mean predicted regression targets of the estimators in the ensemble. Parameters ---------- X : {array-like, sparse matrix} of shape = [n_samples, n_features] The training input samples. Sparse matrices are accepted only if they are supported by the base estimator. Returns ------- y : array of shape = [n_samples] The predicted values. """ check_is_fitted(self, "estimators_features_") # Check data X = check_array(X, accept_sparse=['csr', 'csc']) # Parallel loop n_jobs, n_estimators, starts = _partition_estimators(self.n_estimators, self.n_jobs) all_y_hat = Parallel(n_jobs=n_jobs, verbose=self.verbose)( delayed(_parallel_predict_regression)( self.estimators_[starts[i]:starts[i + 1]], self.estimators_features_[starts[i]:starts[i + 1]], X) for i in range(n_jobs)) # Reduce y_hat = sum(all_y_hat) / self.n_estimators return y_hat def _validate_estimator(self): """Check the estimator and set the base_estimator_ attribute.""" super(BaggingRegressor, self)._validate_estimator( default=DecisionTreeRegressor()) def _set_oob_score(self, X, y): n_samples = y.shape[0] predictions = np.zeros((n_samples,)) n_predictions = np.zeros((n_samples,)) for estimator, samples, features in zip(self.estimators_, self.estimators_samples_, self.estimators_features_): # Create mask for OOB samples mask = ~samples predictions[mask] += estimator.predict((X[mask, :])[:, features]) n_predictions[mask] += 1 if (n_predictions == 0).any(): warn("Some inputs do not have OOB scores. " "This probably means too few estimators were used " "to compute any reliable oob estimates.") n_predictions[n_predictions == 0] = 1 predictions /= n_predictions self.oob_prediction_ = predictions self.oob_score_ = r2_score(y, predictions)